Study

Why are you using a Facebook App?

We use Facebook because of its vast existing social network and as a login mechanism. If someone likes Genes for Good, they can tell their (Facebook) friends. Using Facebook will allow the study to grow both quickly and optimally – through word of mouth. Otherwise, the study is independent of Facebook. That is, Facebook cannot access the information you provide to Genes for Good via the app, such as your survey responses, nor are they involved in our research.

Who can participate?

To participate, you have to be at least 18 years old, live permanently or temporarily in the U.S. with a valid US mailing address, be able to read English fluently, and have a Facebook account.

What are the benefits of this study for myself and for others?

You can view your health history results and compare it to those of others in the study. With the Health Tracking Surveys you can monitor, for example, your physical activity or your stress level. If you provide a saliva sample you will receive information about your ancestry and you can download your raw genetic data. In addition you will contribute to genetic research about common and serious medical conditions and you may find satisfaction in knowing that you are assisting in research that will benefit future generations.

Technical Questions

After the initial agreement to let the app access Facebook it continues to cycle and it never opens. What should I do?

Our app runs inside of Facebook iframe. If your browser only accepts cookies from the site you are visiting this means that Facebook.com works fine but our App (umich.edu) will be blocked as third party. Please make sure either add "umich.edu" to the cookie exception list, or temporarily allow all cookies when you use the App.

I'm trying to use the App on Facebook and it is not working. It worked fine a few days ago.

We have recently migrated our app with new Facebook login workflow and Graphic API v2.0, and this caused some problems. We are working on that.

At this point, you can try a couple of things:

1. Our app runs inside of Facebook iframe. If your browser only accepts cookies from the site you are visiting this means that Facebook.com works fine but our app (umich.edu) will be blocked as third party. Please make sure either add "umich.edu" to the cookie exception list or temporarily allow all cookies when you use the app.

2. If you have successfully used the app in the past, please try deleting cached old history in your browser and load app again.

After clicking the link to receive the results access code several times on different occasions to access results, I have still not received any email with the code.

If the email is not in your spam folder please go to "Your Account - Profile" and check your email address. If this is not your current address, update it and request a new results access code.

I keep getting the message that I've entered the wrong password to access my data.

You may be experiencing a code / link mismatch. Essentially when you request a download link to your raw genetic data we hand that task to a system that bundles your data up, uploads it to Box with the password on it, and emails you the link. If you reset your code then that first link becomes invalid. It will automatically be removed and you should get a new link automatically soon after that's protected with your new code.

Can I download the raw data files to an iPad?

When you are on an iPad then you should be served the mobile site, which does not have the download option built out (or any parts of the ancestry data aside from the pie chart). We're working on a new module site but for now you can only access the files from a desktop computer.

Surveys

What is the difference between Health History and Health Tracking Surveys?

Health History and Health Tracking are the two ways we ask about health information in Genes for Good. Health History Surveys focus, for example, on lifelong health, such as whether you've ever had cancer or a heart attack. All Health Tracking Surveys are meant to be completed routinely – every day, several times per week, however often you can spare a few minutes.

Do I have to do the Health Tracking Surveys every day?

Although we would appreciate it if you fill out the Health Tracking Surveys every day, you don’t have to. You can also do the surveys in larger intervals, for example two times per week.

Why are there only plots for two or three questions for each survey? For one Health Tracking Survey there is no plot at all.

To begin with we picked two or three questions from each survey to show study results. We will add more plots over time.

Consent Form

You can find instructions for filling out the consent form here under Step 1: Study Information and Consent Form.

Why can’t I get past the first page of the online consent form (15 %)? When I click NEXT it keeps looping back.

It is possible that your Facebook email address ends with “@tfbnw.net”. If this is the case please go to the General Account Settings on your Facebook page and enter a different email address.

You could also try using a different internet browser.

Why do I have to sign a hardcopy consent form before giving a saliva sample? I’ve already consented online.

The online consent form is to participate in the online surveys only. To analyze your saliva sample for genetic research we need written consent - that means your signature and the date on a paper consent form.

Participation

I don’t live in the US. Can I still participate?

Unfortunately, no. For now we are only allowed to have participants who live in the US.

How do I consent to participate in the study?

For the online surveys you can only consent online. Please use the "Next" button to click through the pages of the consent form. On the last page check the little box at the bottom if you are 18 years of age or older and live currently in the US. After clicking "Accept" you will be able to continue.

I'm using a fake name for my Facebook account. Do I have to use my real name to participate in Genes for Good?

When you choose to submit a saliva sample we will send you a hardcopy consent form for signature. The name on the consent form has to match the name in our database so please enter your real name under "Your Account" - "Profile".

Can I stop participating in the surveys if I don't want to continue?

You can stop participating at any time. You can stop answering surveys or you can delete the App from your Facebook Account. Please note that if you delete the App we will not be able to notify you about new surveys or results. If you not only want to stop but withdraw from the study, please see the question below.

How can I withdraw from the study?

You can withdraw from Genes for Good at any time. You can stop participating in the study by using the withdrawal link in the App which can be found under “Your Account” in the upper right corner. Withdrawing is also possible by contacting us, or by calling us at (734) 647-7773. Only you can remove the Genes for Good App from your Facebook account, which you can do through your Facebook Account Settings page.

Will you keep any information after I withdraw?

After withdrawing we will keep your survey responses and delete your name and unique Facebook ID from our database. We will also remove your addresses (IP address and physical address) and phone number (if you provided them to us). We will keep your age, sex, and zip code, and use these limited data for future research; this includes also your DNA, if you have provided a sample.

What are the risks of participating?

For participation in online surveys only: There is only minimal risk in participating in the online surveys. The only direct risk involves a breach in data security. It is possible, though we consider it unlikely, that our web-based server and standalone data server security would be jointly compromised, in which case identifiable responses to health- and behavior-related questions could be discovered.

For donating a saliva sample: If you participate in genetic research and submit a saliva sample, a breach in data security is again one direct risk. We have taken important steps to reduce this risk, including the utilization of separate independent servers to host the web application and your responses and genetic data. If the genetic information is used in some way to identify you, it is possible that you could suffer psychological or emotional harm, or other unforeseen consequences. The Genetic Information Nondiscrimination Act of 2008 (GINA) is a federal law that protects individuals from genetic discrimination in health insurance and employment. You can find more information about GINA here.

We will provide you with information about your ancestry based on DNA analysis. The primary anticipated significant risk associated with receipt of this information is discovery or suspicion of nonpaternity and/or secret adoption. That is, discovering one's ancestry is inconsistent with what you know about the ancestry of your supposedly biological parents. This is in fact a risk of any genetic test, and we provide education about this risk during the informed consent. If you remain concerned about the implications of the test for your family relationships, we encourage you to contact a genetic counselor.

I do not want to participate through Facebook. Is there an alternative besides the Facebook app?

Right now there is no other way to participate.

Spit Kits

How do I become eligible for a spit kit?

You will qualify for a spit kit by completing 15 Health History Surveys and 20 of the Health Tracking Surveys.

How can I request a spit kit?

You don’t have to request it. After you have completed the required number of surveys and have entered your age group and address, you will automatically be added to our spit kit mailing list. You can check your eligibility progress by viewing the progress bar on the app homepage.

When will my spit kit arrive?

Please allow up to two weeks to receive your kit. You can see in the “Spit Kit Status” under “Your Account” if the spit kit has been sent.

Please use the included return envelope to send your sample back with USPS.

Results

How long does it take to receive the results after a spit kit has been submitted?

Our current turnaround time is two to three months after we send the sample to the lab. It depends on the amount of incoming samples and on the outcome of the quality controls.

What are the timelines for the different steps from being eligible for a spit kit to receiving results?

1) Receiving the spit kit: When you become eligible for a spit kit we will mail it to you in the following two weeks. You can check the "Spit Kit Status" on your Genes for Good app homepage. It can take up to two weeks to receive it.

2) When we receive it back from you we enter the date when it returned to us. Sending it back to us can also take up to two weeks.

3) In the next step we check the consent form (name, signature, and date) and the saliva sample (amount), and forward the sample to the lab. You will see new information in your "Spit Kit Status".

4) The lab extracts and genotypes the DNA. We will do many quality checks to make sure that participants receive correct results. If there's not enough DNA in your saliva sample or if the results don't pass quality controls, we will contact you and send you another spit kit. Our current turnaround time for results is two to three months after we send the sample to the lab. You will receive an additional notification when the data is available to download securely through the app.

About the ancestry estimation, how much detail will you be providing - will that include admixture percentages etc?

We will provide three pieces of information:

1. Estimated percentage of your DNA from each of the 7 major world populations: Europe, Africa, East Asia, Central/South Asia, West Asia/North Africa, Americas, and Oceania. We may choose to round these percentages to 1/16ths or 1/32nds to reflect likely proportions of admixture and reduce noise in the estimates.

2. A plot of your chromosomes, showing the most likely ancestral population for each of your chromosomal segments.

3. A plot showing where the principal components of your genotypes fall relative to the 7 major world populations.

Do I have the ability to select any data/results that I do not want shown - for example if I have Parkinson’s Disease or a risk for another disease?

Currently, we only have approval to show you (a) information about your ancestry and (b) your raw genetic data. We will not give you any information about the risk for a specific disease.

Will there be a mechanism for those of us who volunteer to be kept abreast of findings, aggregate data analysis, trends etc.?

In our monthly newsletter, we will update you on any major developments -- we hope that knowing how your information is being used will be reassuring and provide some motivation to stay engaged with the study.

When I download my raw data will it be compatible with Family Tree DNA, 23andMe, Ancestry.com, etc.? If not any of those platforms, what format will it be presented in?

We use a VCF file, which is a standard format for exchanging genetic data. A VCF file is a text file format used in bioinformatics for storing gene sequence variations. It contains a header section with meta-information lines and a data section with about 500,000 lines each containing information about a position in your genome. We are not sure if 23andMe and Ancestry.com allow you to upload your own genetic data (or if they only analyse data they generate), but VCF is a very widely used format. There are community sites that will interpret VCF files.

Is it possible to upload my 23andMe or Ancestry.com data?

We have discussed giving participants the option to share their genotypes from other services like Ancestry.com or 23andMe. This would actually save our costs considerably and allow us to recruit more individuals for genetic study. We have not done a lot of work on providing a secure way for participants to do this yet, but we would like to implement this in the future.

Is it possible to upload Whole Genome Sequencing (WGS) files in addition to 23andMe files? If yes, do you have preference for data formats?

We are curious about allowing this, and will have to figure out how to gauge how many people would be interested in donating / sharing their data in this way. In the short term, a VCF file seems appealing (a BAM/CRAM would provide the most long-term flexibility but might be cumbersome to transfer).

Do you also provide the haplogroup?

The Y and MT genotypes may have sufficient information to determine haplogroups but we have not looked into this yet. This is something that definitely needs more work. So probably not in the near future.

Can the results be mailed to my house or sent by email?

No. The approved ways of accessing your results are the Genes for Good app for the ancestry results, and Box for downloading your raw genetic data.

Is your lab CLIA certified?

No. Genes for Good is a research study and the technology and protocols we use are suitable for genetic research only, not for clinical genetic testing like you would receive at a hospital or doctor's office. Clinical genetic testing is held to higher standards and is done in laboratories, which are certified by governmental regulations called CLIA (Clinical Laboratory Improvement Amendments). If you use the Genes for Good data for diagnostic purposes, you should always have it confirmed by a real genetic test.

Research

What will this project use my information for?

With the information you give us by answering surveys and your DNA, we can do genetic association studies. We are trying to understand how genetic mutations cause diseases and how genes interact with the environment to result in diseases.

Which genetic variants will be genotyped?

The sample VCF file (19.5Mb) UM_GenesforGood_v1.2_genotyped_variant_list_sample_vcf.txt contains preliminary information about the genetic variants that we will genotype for each participant. Since the genotype data will undergo extensive quality control, the final list of informative/genotyped variants might be somewhat smaller.

I am involved in a project that is going to offer WGS for consumer early adopters interested in preventative health/fitness/nutrition and we would like to be sure that whatever annotation/bioinformatics we do is optimized for applications like Genes for Good so consumers can easily upload their files (from cloud based storage) to your web site.

We don't have a preference as to whether dbSNP rs#s are included. We would probably recommend build 37 in the short run, and build 38 as a longer term option (build 37 will likely become obsolete soon). We probably would recommend using a tool like vt to ensure variants are represented in a unique way -- some variants can be represented in many different ways.

Data safety

Who can see my responses?

Only study personnel can see your responses and only very few trusted individuals have additional access to your identifiers, such as your name. This means that people who analyze your responses don’t know who you are; they only have a study number that we assigned to you.

Can Facebook see my responses?

No, Facebook cannot see your responses. The App uses a database and a web server, located at our department at the University of Michigan, to deliver questions to you. We use a second data server to securely store the responses. Only study personnel have access to these servers.

Can Facebook see anything related to this study?

Facebook can see whether and when you are using the App. They cannot see your responses, summary information, or genetic information.

How do you keep my identity confidential when you share data with other researchers?

When we share data we de-identify them. We will give your data a study number and that is all other researchers will get. No names, no addresses.

How is my privacy protected?

While logged into the App your privacy is protected through industry-standard electronic security. Your data will be protected on a secure server that is not directly connected to the public internet. All data on this server will be de-identified to protect your privacy. Facebook cannot access the information collected through the App, even if you are logged in on Facebook while answering surveys. The same also applies for your summary information and genetic information. DNA samples are stored in suitable locations on the University of Michigan campus. All samples are bar-coded and de-identified. Sample handling, processing, and storage activities occur in physically secure, locked spaces, with access restricted to authorized personnel only.

How closely do the privacy safeguards and consent agreements mirror what the NIH provides?

The NIH uses a variety of consent and data sharing agreements -- some are more restrictive than ours (for example, because they target populations who are at very special risk or focus on conditions like AIDS, etc.) others that are more open (for example, that allow the data to be shared directly on the internet without restrictions on use). We tried to balance things by saying that data has more value if more researchers try to analyze it, by separating more personal information from the rest [e.g. name, address, phone number], and by requiring that anyone who uses the data should not try to identify you.

The Henrietta Lacks case was troubling. Is there any chance that my genetic data/sample could be used for similar purposes?

There are many troubling aspects of the Henrietta Lacks case. Henrietta Lacks was a black woman whose cervical cancer cells were harvested without her permission and used to create the HeLa immortal cell line. Neither she nor her family received any direct benefits from the research done with her cells, nor were they ever informed by Johns Hopkins that the cells were taken and used. In our case, from a saliva sample, we would be collecting DNA, not cells, and we have no plans (or technical means) to establish immortal cell lines based on the sample you provide. However, a sample you provide hopefully will be used for research (by us and others) and you should expect no direct benefit of downstream discoveries, which may be seen as similar to the Henrietta Lacks case, but we are informing you and asking for your consent to use your samples.

Will Facebook the corporation have access or be privy to my genetic results - other than what is listed on the site by me or your organization? Is there any agreement with Facebook that prohibit them from selling this data? I am not worried about those who I allow to see my data, I am worried about Facebook scraping my data off the Facebook page and selling it or using it to market drugs etc. to me.

Facebook should not see your genetic results, they don't sit on Facebook servers and we will always transmit them via encrypted connection -- e.g. we don't think they could be scraped.